Can't quite find this in the rules, what happens when a cultist is supposed to be added to the same spot as a shoggoth? Does it trigger another awakening? Also does the hunter not get a relic card for killing a shoggoth since it's only one action?

Hmm... As far as the third question the rule book states "a player who uses three actions to defeat a shoggoth immediately draws a relic card" the Hunter only uses one action so that's why I'm not sure.